Project

General

Profile

Bug #1626

trjcat segfaults when converting xtc/trr -> tng

Added by Jan-Philipp Machtens over 2 years ago. Updated over 2 years ago.

Status:
Closed
Priority:
Low
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

Dear developers,
(Version : 5.0.2)
converting xtc or trr file(s) to tng format usign trjcat results
in "Segmentation fault (core dumped).
Converting tng file(s) to xtc with trjcat works.
Concatenating tng file(s) to one single tng works.
Other gmx modules, including trjconv, seem to work well with tng.

I suspect the reason for that is the "molecule block" at the beginning of the tng (DOI: 10.1002/jcc.23495),
which trjcat tries to fill up. This is impossible for "trjcat -f xtc -o tng", since trjcat does not accept
tpr files as input such that trjcat cannot know the details about molecules/atoms.
In contrast, trjconv behaves well:
"trjconv -f t1.xtc -o t2.xtc" runs without topol.tpr
but "trjconv -f t1.xtc -o t2.tng" will ask for an additional "-s topol.tpr input" in order to get the information for the "molecule block" of the tng file.

IMHO, trjcat does not necessarily need to capability for xtc->tng conversion, therefore it might be sufficient
to change the documentation and prevent the combination of xtc input and tng output for trjcat ?

Associated revisions

Revision ac83c85a (diff)
Added by Magnus Lundborg over 2 years ago

When writing TNG the input must contain molecule data.

When using trjcat to write TNG the input must also be TNG since
no tpr file is used.

Fixes #1626

Change-Id: I060e0174f9a471e134a4a899f83afaf02f4fce00

History

#1 Updated by Erik Lindahl over 2 years ago

  • Assignee set to Magnus Lundborg

#2 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #1626.
Uploader: Magnus Lundborg ()
Change-Id: I060e0174f9a471e134a4a899f83afaf02f4fce00
Gerrit URL: https://gerrit.gromacs.org/4175

#3 Updated by Mark Abraham over 2 years ago

  • Status changed from New to Resolved

Indeed Jan, trjcat has now been modified to require TNG input in order to produce TNG output. Thanks!

#4 Updated by Mark Abraham over 2 years ago

  • Status changed from Resolved to Closed
  • Target version changed from 5.x to 5.0.5

Was fixed in 5.0.4, actually

Also available in: Atom PDF